mean over what? a parcellation? an activation cluster?

On 10/31/2019 3:15 PM, Amrita Bedi wrote:

External Email - Use Caution

Thank you Dr Greve, that issue is resolved.

I do have another question. I’m now trying to extract mean correlation values to the seed from each individual subject and not sure how to go about this.

On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz file correctly Try mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz

Where you have "bilat*", that should only be one folder

On 10/31/19 12:04 PM, Amrita Bedi wrote:

    External Email - Use Caution

---------- Forwarded message ---------- From: *abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu>* <abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu>> Date: Thursday, October 31, 2019 Subject: Fw: glm error To: Amrita Bedi <amibedi273@gmail.commailto:amibedi273@gmail.com <mailto:amibedi273@gmail.commailto:amibedi273@gmail.com>>

Amrita Bedi /Biomedical Engineering - Class of 2018/ /The City College of New York - CUNY/

---

*From:* abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu> *Sent:* Thursday, October 31, 2019 12:02 PM *To:* Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> <Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>> *Subject:* glm error Hello Freesurfer developers,

I ran a seed based resting stage functional analysis for 287 subjects using the isthmus of the cingulate as a seed and now have pcc.nii.gz files in each individual subject folder. I concatenated these pcc files and am trying to run an osgm but get the following error: ERROR: DOF = 0 The commands i ran for concatenating and glm are: for l in `cat sessidBOLD2`; do mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; done

mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir

The mriglmfit.log gave me the following:

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/FSFAST cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir sysname Linux hostname imaging5.vaboston.lan machine x86_64 user root FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz logyflag 0 usedti 0 labelmask /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label maskinv 0 glmdir all_subjects_lh_ic_pcc.TR3.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0

Thank you for your help.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

you mean the average across all activations or clusters of activation?

On 10/31/2019 9:18 PM, Amrita Bedi wrote:

External Email - Use Caution

Mean correlation values to the seed from activations of a pcc.mgh map from each individual subject.

On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: mean over what? a parcellation? an activation cluster?

On 10/31/2019 3:15 PM, Amrita Bedi wrote:

External Email - Use Caution

Thank you Dr Greve, that issue is resolved.

I do have another question. I’m now trying to extract mean correlation values to the seed from each individual subject and not sure how to go about this.

On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz file correctly Try mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz

Where you have "bilat*", that should only be one folder

On 10/31/19 12:04 PM, Amrita Bedi wrote:

    External Email - Use Caution

---------- Forwarded message ---------- From: *abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu>* <abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu>> Date: Thursday, October 31, 2019 Subject: Fw: glm error To: Amrita Bedi <amibedi273@gmail.commailto:amibedi273@gmail.com <mailto:amibedi273@gmail.commailto:amibedi273@gmail.com>>

Amrita Bedi /Biomedical Engineering - Class of 2018/ /The City College of New York - CUNY/

---

*From:* abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu> *Sent:* Thursday, October 31, 2019 12:02 PM *To:* Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> <Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>> *Subject:* glm error Hello Freesurfer developers,

I ran a seed based resting stage functional analysis for 287 subjects using the isthmus of the cingulate as a seed and now have pcc.nii.gz files in each individual subject folder. I concatenated these pcc files and am trying to run an osgm but get the following error: ERROR: DOF = 0 The commands i ran for concatenating and glm are: for l in `cat sessidBOLD2`; do mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; done

mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir

The mriglmfit.log gave me the following:

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/FSFAST cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir sysname Linux hostname imaging5.vaboston.lan machine x86_64 user root FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz logyflag 0 usedti 0 labelmask /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cohttp://lh.cortex.label maskinv 0 glmdir all_subjects_lh_ic_pcc.TR3.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0

Thank you for your help.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

First create a mask of your activation mri_binarize --i sig.mgh --min 2 --o sig.mask2.mgh 2 here is the threshold in -log10(p) (so 2 mean p<.01)

next cd session/bold/analysis/contrast mri_segstats --i pcc.nii.gz --id 1 --seg /path/to/sig.mask2.mgh --sum sum.dat The mean pcc will be in the "Mean" column

On 11/1/2019 12:16 PM, Amrita Bedi wrote:

External Email - Use Caution

Across all activations since the pcc map was generated by an osgm.

On Friday, November 1, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: you mean the average across all activations or clusters of activation?

On 10/31/2019 9:18 PM, Amrita Bedi wrote:

External Email - Use Caution

Mean correlation values to the seed from activations of a pcc.mgh map from each individual subject.

On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: mean over what? a parcellation? an activation cluster?

On 10/31/2019 3:15 PM, Amrita Bedi wrote:

External Email - Use Caution

Thank you Dr Greve, that issue is resolved.

I do have another question. I’m now trying to extract mean correlation values to the seed from each individual subject and not sure how to go about this.

On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz file correctly Try mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz

Where you have "bilat*", that should only be one folder

On 10/31/19 12:04 PM, Amrita Bedi wrote:

    External Email - Use Caution

---------- Forwarded message ---------- From: *abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu>* <abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu>> Date: Thursday, October 31, 2019 Subject: Fw: glm error To: Amrita Bedi <amibedi273@gmail.commailto:amibedi273@gmail.com <mailto:amibedi273@gmail.commailto:amibedi273@gmail.com>>

Amrita Bedi /Biomedical Engineering - Class of 2018/ /The City College of New York - CUNY/

---

*From:* abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edumailto:abedi000@citymail.cuny.edu> *Sent:* Thursday, October 31, 2019 12:02 PM *To:* Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> <Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>> *Subject:* glm error Hello Freesurfer developers,

I ran a seed based resting stage functional analysis for 287 subjects using the isthmus of the cingulate as a seed and now have pcc.nii.gz files in each individual subject folder. I concatenated these pcc files and am trying to run an osgm but get the following error: ERROR: DOF = 0 The commands i ran for concatenating and glm are: for l in `cat sessidBOLD2`; do mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; done

mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir

The mriglmfit.log gave me the following:

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/FSFAST cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir sysname Linux hostname imaging5.vaboston.lan machine x86_64 user root FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz logyflag 0 usedti 0 labelmask /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cohttp://lh.cortex.label maskinv 0 glmdir all_subjects_lh_ic_pcc.TR3.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0

Thank you for your help.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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